Contacts of the helix formed by residues 79 - 92 (chain D) in PDB entry 1RX0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 79 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLN* 4.6 1.6 + - - -
68D TYR* 5.0 0.7 - - - -
78D LEU* 1.3 72.7 - - - +
80D ARG* 1.3 60.0 + - - +
81D LEU* 3.5 8.7 + - - +
82D ASP* 2.7 39.1 + - - -
83D THR* 2.9 32.3 + - - -
319D GLN* 3.3 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D TYR* 3.3 39.1 + - - +
79D SER* 1.3 74.9 - - - +
81D LEU* 1.3 57.7 + - - +
83D THR* 3.4 6.9 + - - -
84D SER* 2.9 28.1 + - - -
109D TRP* 3.4 40.6 - - - +
249D ARG 5.5 1.6 + - - -
250D GLY 5.6 0.2 + - - -
253D GLY* 3.6 24.0 - - - -
256D ILE* 5.0 4.5 - - + +
257D ASN* 4.9 4.6 - - - +
315D ALA* 3.4 26.3 - - + +
318D LEU* 4.0 25.1 + - + +
319D GLN* 3.0 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 4.8 2.2 - - + -
23D GLN* 3.6 26.2 - - - +
79D SER* 3.2 7.9 + - - +
80D ARG* 1.3 77.2 - - - +
82D ASP* 1.3 64.9 + - - +
84D SER* 3.3 3.1 + - - -
85D VAL* 3.1 32.9 + - + +
312D ARG* 3.6 48.5 - - + +
315D ALA* 3.8 11.7 + - + +
316D VAL* 4.0 22.7 - - + +
319D GLN* 5.3 1.0 - - + +
9007D ACY 3.9 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ASN* 5.0 0.2 + - - -
22D GLU* 5.5 2.9 - - - +
23D GLN* 2.9 36.9 + - - +
26D PHE* 4.0 22.3 - - + -
78D LEU* 3.6 21.9 - - + +
79D SER* 2.7 40.0 + - - +
81D LEU* 1.3 75.6 - - - +
83D THR* 1.3 62.2 + - - +
85D VAL* 3.3 7.8 + - - +
86D ILE* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL* 3.3 25.4 - - + +
68D TYR* 3.5 30.4 - - + +
78D LEU 4.5 0.2 + - - -
79D SER 2.9 18.1 + - - -
80D ARG* 3.5 8.3 - - - -
82D ASP* 1.3 74.7 - - - +
84D SER* 1.3 65.1 + - - +
86D ILE* 3.1 4.1 + - - +
87D PHE* 2.9 54.6 + - + +
257D ASN* 3.6 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ARG 2.9 18.0 + - - -
81D LEU* 3.6 12.1 - - - -
83D THR* 1.3 75.8 - - - +
85D VAL* 1.3 58.2 + - - +
87D PHE 3.5 0.2 + - - -
88D GLU* 3.0 32.4 + - - +
256D ILE* 4.5 8.1 - - - -
257D ASN* 4.2 4.4 + - - -
260D SER* 2.7 29.8 + - - -
263D LEU* 4.9 3.3 - - - +
311D VAL* 3.4 16.5 - - - +
312D ARG* 4.5 9.1 + - - +
315D ALA* 4.6 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.8 34.1 - - + -
23D GLN* 4.1 8.7 - - + +
26D PHE* 5.4 1.3 - - + -
27D GLN* 3.6 43.5 - - + +
81D LEU* 3.1 19.3 + - + +
82D ASP* 3.5 10.5 - - - +
84D SER* 1.3 75.9 - - - +
86D ILE* 1.3 63.8 + - + +
88D GLU* 3.7 9.8 - - - +
89D ALA* 3.1 22.7 + - - +
312D ARG* 4.2 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PHE* 4.1 26.7 - - + +
27D GLN* 5.6 0.2 - - - +
30D ALA* 3.9 7.6 - - + +
64D PHE* 3.7 41.1 - - + -
67D VAL* 3.8 15.0 - - + -
78D LEU* 3.7 28.9 - - + -
82D ASP 3.1 15.5 + - - +
83D THR* 3.1 7.2 + - - +
85D VAL* 1.3 74.1 - - - +
87D PHE* 1.3 67.6 + - + +
89D ALA* 3.2 3.5 + - - +
90D LEU* 2.9 41.1 + - + +
9003D ACY 4.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D PHE* 4.8 0.7 - - + -
67D VAL* 4.3 14.1 - - + -
68D TYR* 4.7 1.6 - + - -
83D THR* 2.9 36.7 + - + +
84D SER 4.1 2.0 - - - +
86D ILE* 1.3 75.1 - - + +
88D GLU* 1.3 60.1 + - - +
90D LEU* 4.2 9.4 - - + -
91D ALA* 2.8 32.3 + - - +
98D THR* 3.4 23.3 - - + +
101D ILE* 3.9 20.2 - - + -
102D SER* 3.6 35.4 - - - -
105D ASN* 3.9 17.9 - - - -
257D ASN* 3.5 34.1 - - + +
260D SER* 4.2 12.1 - - - -
261D CYS* 4.5 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLN* 4.5 2.8 - - - +
84D SER* 3.0 17.9 + - - +
85D VAL* 3.7 9.0 - - - +
87D PHE* 1.3 78.0 - - - +
89D ALA* 1.3 63.9 + - - +
91D ALA 3.4 3.1 + - - -
92D THR* 3.6 4.2 - - - +
260D SER* 3.3 19.9 + - - +
263D LEU* 3.6 21.3 - - + +
264D GLY* 3.2 34.0 - - - +
308D ARG* 2.8 38.8 + - - -
312D ARG* 2.9 27.9 + - - -
2009D EDO 3.7 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLN* 4.0 10.8 - - + +
30D ALA* 3.7 20.0 - - + -
31D PHE* 3.9 13.3 - - - +
34D ALA* 3.7 6.5 - - - +
85D VAL 3.1 16.7 + - - +
86D ILE 3.6 3.8 - - - +
87D PHE 3.2 0.2 - - - -
88D GLU* 1.3 80.8 - - - +
90D LEU* 1.3 58.5 + - - +
92D THR* 2.6 27.2 + - - -
2009D EDO 4.2 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ALA* 3.6 28.3 - - + +
33D PHE* 3.9 23.6 - - + -
34D ALA* 3.8 3.4 - - + +
38D MET* 3.6 12.6 - - + +
59D ALA* 5.6 0.7 - - + -
64D PHE* 3.9 23.1 - - + -
86D ILE* 2.9 36.0 + - + +
87D PHE* 4.2 14.4 - - + -
89D ALA* 1.3 75.9 - - - +
91D ALA* 1.3 58.1 + - - +
93D GLY* 2.9 20.1 + - - -
94D CYS 3.4 5.4 + - - -
98D THR* 3.1 24.8 + - + +
101D ILE* 4.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE 2.8 18.1 + - - +
88D GLU 3.6 6.7 - - - +
89D ALA 3.2 0.4 - - - -
90D LEU* 1.3 75.5 - - - +
92D THR* 1.3 61.4 + - - +
93D GLY 3.1 0.6 + - - -
94D CYS 3.5 3.3 + - - -
95D THR* 3.0 32.3 + - - +
98D THR* 3.3 10.9 + - - -
261D CYS* 3.4 39.3 - - + +
264D GLY* 4.0 4.3 - - - -
265D ALA 4.4 0.5 + - - -
365D TYR* 4.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PHE* 3.6 23.1 - - + -
34D ALA* 4.1 2.9 - - - +
39D ALA* 5.0 3.8 - - - +
88D GLU 3.6 9.0 - - - +
89D ALA 2.6 17.6 + - - +
90D LEU 3.1 0.2 - - - -
91D ALA* 1.3 77.9 - - - +
93D GLY* 1.3 58.2 + - - +
264D GLY 3.5 22.4 - - - +
267D HIS* 5.0 2.0 - - + +
268D ALA* 4.2 16.7 - - + +
365D TYR* 2.7 25.0 + - - -
2009D EDO 3.5 29.4 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il